10  Gene Enrichment Analysis II

Removed Mitochondria-Related Genes from DESeq2 Results

Published

November 5, 2025

To identify biological pathways and processes affected by Cre-mediated ApoE4→ApoE2 conversion in liver tissue, we performed complementary enrichment analyses using the high-confidence differentially expressed genes from Method 1 (combined batches, no batch adjustment).

The mouse mitochondrial genome encodes 37 genes in total:

mitochondrial genes found (and removed) from the dataset:

[1] "mt-Rnr1, mt-Rnr2, mt-Nd1, mt-Nd2, mt-Co1, mt-Ts1, mt-Co2, mt-Atp8, mt-Atp6, mt-Co3, mt-Nd3, mt-Nd4, mt-Nd5, mt-Nd6, mt-Cytb, mt-Nd4l"

10.0.1 Gene Set Enrichment Analysis (GSEA)

pathway NES padj size
GOBP_TRANSLATION_AT_SYNAPSE 2.092 0.031 48
GOBP_MITOCHONDRIAL_RESPIRATORY_CHAIN_COMPLEX_ASSEMBLY 2.024 0.026 96
GOBP_NADH_DEHYDROGENASE_COMPLEX_ASSEMBLY 1.990 0.037 57

Gene Set Enrichment Analysis (GSEA) using the complete ranked gene list (without the mitochondrial genes) identified 3 significantly enriched pathways.

These pathways encompassed translation at the synapse (NES = 2.092, padj = 0.031), mitochondrial respiratory chain complex assembly (NES = 2.024, padj = 0.026), and NADH dehydrogenase complex assembly (NES = 1.990, padj = 0.037), suggesting that hepatic ApoE2 expression modulates both synaptic protein synthesis and mitochondrial oxidative capacity.

10.1 Brain

10.1.1 Gene Set Enrichment Analysis (GSEA)

pathway NES padj size
GOBP_EPOXYGENASE_P450_PATHWAY 2.155 0.015 26
GOBP_ARACHIDONIC_ACID_METABOLIC_PROCESS 2.136 0.009 59
GOBP_REGULATION_OF_CHROMATIN_ORGANIZATION 2.130 0.015 35
GOBP_XENOBIOTIC_METABOLIC_PROCESS 2.125 0.002 98
GOBP_SPLICEOSOMAL_COMPLEX_ASSEMBLY 2.068 0.015 49
GOBP_URONIC_ACID_METABOLIC_PROCESS 2.063 0.031 15
GOBP_RESPONSE_TO_PROSTAGLANDIN 2.049 0.048 22
GOBP_POSITIVE_REGULATION_OF_MRNA_CATABOLIC_PROCESS 1.877 0.029 91
GOBP_POSITIVE_REGULATION_OF_MRNA_METABOLIC_PROCESS 1.857 0.015 125
GOBP_REGULATION_OF_MRNA_PROCESSING 1.843 0.018 129
GOBP_DENDRITE_MORPHOGENESIS 1.833 0.003 188
GOBP_CELLULAR_RESPONSE_TO_XENOBIOTIC_STIMULUS 1.831 0.015 153
GOBP_REGULATION_OF_MRNA_METABOLIC_PROCESS 1.814 0.002 274
GOBP_ACTION_POTENTIAL 1.806 0.009 160
GOBP_NEGATIVE_REGULATION_OF_GENE_EXPRESSION_EPIGENETIC 1.738 0.025 145
GOBP_DENDRITE_DEVELOPMENT 1.699 0.005 315
GOBP_RESPONSE_TO_ALCOHOL 1.651 0.038 166
GOBP_SYNAPSE_ASSEMBLY 1.607 0.016 267
GOBP_POSTSYNAPSE_ORGANIZATION 1.574 0.022 283
GOBP_CHROMATIN_REMODELING 1.521 0.003 472
GOBP_REGULATION_OF_SYNAPSE_STRUCTURE_OR_ACTIVITY 1.455 0.031 365
GOBP_MRNA_PROCESSING 1.438 0.015 453

GSEA of brain tissue revealed 22 significantly enriched pathways.

10.1.1.1 Reducing Redundant Pathways with collapsePathways

Given the extensive overlap in leading-edge genes between pathways, we applied the collapsePathways function from the fgsea package to reduce redundancy and identify independent biological themes. This analysis groups pathways with highly similar gene membership, retaining only the most significantly enriched representative from each cluster.

pathway NES padj size
GOBP_REGULATION_OF_CHROMATIN_ORGANIZATION 2.130 0.015 35
GOBP_XENOBIOTIC_METABOLIC_PROCESS 2.125 0.002 98
GOBP_SPLICEOSOMAL_COMPLEX_ASSEMBLY 2.068 0.015 49
GOBP_REGULATION_OF_MRNA_METABOLIC_PROCESS 1.814 0.002 274
GOBP_ACTION_POTENTIAL 1.806 0.009 160
GOBP_DENDRITE_DEVELOPMENT 1.699 0.005 315
GOBP_RESPONSE_TO_ALCOHOL 1.651 0.038 166
GOBP_SYNAPSE_ASSEMBLY 1.607 0.016 267
GOBP_CHROMATIN_REMODELING 1.521 0.003 472
GOBP_REGULATION_OF_SYNAPSE_STRUCTURE_OR_ACTIVITY 1.455 0.031 365

This analysis yielded 10 representative pathways that captured the major biological processes altered by hepatic ApoE2 expression. The collapsed pathway set retained the most significantly enriched representatives, including chromatin organization and remodeling, xenobiotic and metabolic processes, splicing and mRNA processing, neuronal development, and synaptic function, thereby providing a streamlined view of the fundamental biological processes affected by selective hepatic ApoE isoform conversion.